[ENH] improve log and change verbosity parameter

.codespellrc

@@ -0,0 +1,4 @@
+[codespell]
+skip = .git,env,build,outputs,.mypy_cache,moae_fmriprep
+ignore-words-list = fo
+builtin = clear,rare

.pre-commit-config.yaml

@@ -41,7 +41,7 @@ repos:
         rev: 'v0.991'
         hooks:
         -   id: mypy
-            additional_dependencies: [types-all]
+            additional_dependencies: [types-all, pydantic]
             files: bidsmreye
             args: ["--config-file", "setup.cfg"]
 

Makefile

@@ -135,28 +135,29 @@ clean-demo:
 	rm -fr outputs/moae_fmriprep
 
 demo: clean-demo tests/data/moae_fmriprep ## demo: runs all demo steps on MOAE dataset
-	bidsmreye 	--action all \
-				$$PWD/tests/data/moae_fmriprep \
+	bidsmreye	$$PWD/tests/data/moae_fmriprep \
 				$$PWD/outputs/moae_fmriprep/derivatives \
-				participant
+				participant \
+				--action all \
+				-vv \
 
 prepare: tests/data/moae_fmriprep ## demo: prepares the data of MOAE dataset
-	bidsmreye 	--action prepare \
-				--verbosity INFO \
-				--debug true \
-				--reset_database true \
-				$$PWD/tests/data/moae_fmriprep \
+	bidsmreye 	$$PWD/tests/data/moae_fmriprep \
 				$$PWD/outputs/moae_fmriprep/derivatives \
-				participant
+				participant \
+				--action prepare \
+				-vv \
+				--debug \
+				--reset_database
 
 generalize: ## demo: predicts labels of MOAE dataset
-	bidsmreye 	--action generalize \
-				--verbosity WARNING \
-				--debug true \
-				--reset_database true \
-				$$PWD/tests/data/moae_fmriprep \
+	bidsmreye 	$$PWD/tests/data/moae_fmriprep \
 				$$PWD/outputs/moae_fmriprep/derivatives \
-				participant
+				participant \
+				--action generalize \
+				-vv \
+				--debug \
+				--reset_database
 
 
 ## Openneuro data
@@ -173,35 +174,37 @@ get_ds002799: tests/data/data_ds002799
 	datalad get sub-30[27]/ses-*/func/*run-*preproc*bold*
 
 ds002799_prepare: get_ds002799
-	bidsmreye 	--action prepare \
-				--debug true \
-				$$PWD/tests/data/ds002799/derivatives/fmriprep \
+	bidsmreye 	$$PWD/tests/data/ds002799/derivatives/fmriprep \
 				$$PWD/outputs/ds002799/derivatives \
 				participant \
+				--action prepare \
+				--debug \
 				--participant_label 302 307 \
 				--space MNI152NLin2009cAsym T1w \
 				--run 1 2
 
+
 ds002799_generalize:
-	bidsmreye 	--action generalize \
-				--debug true \
-				$$PWD/tests/data/ds002799/derivatives/fmriprep \
+	bidsmreye 	$$PWD/tests/data/ds002799/derivatives/fmriprep \
 				$$PWD/outputs/ds002799/derivatives \
 				participant \
+				--action generalize \
+				--debug \
 				--participant_label 302 307 \
 				--space MNI152NLin2009cAsym T1w \
 				--run 1 2
 
+
 ds002799: clean-ds002799 get_ds002799
-	bidsmreye 	--action all \
-				--debug true \
-				$$PWD/tests/data/ds002799/derivatives/fmriprep \
+	bidsmreye	$$PWD/tests/data/ds002799/derivatives/fmriprep \
 				$$PWD/outputs/ds002799/derivatives \
 				participant \
+				--action all \
+				--debug \
 				--participant_label 302 307 \
 				--space MNI152NLin2009cAsym T1w \
-				--run 1 2
-
+				--run 1 2 \
+				-vv
 
 ## DOCKER
 .PHONY: docker/Dockerfile docker/Dockerfile_dev
@@ -276,8 +279,8 @@ docker_prepare_data:
 				/home/neuro/outputs/ \
 				participant \
 				--action prepare \
-				--debug true \
-				--reset_database true
+				--debug \
+				--reset_database
 
 docker_generalize:
 	docker run --rm -it \

bidsmreye/run.py → bidsmreye/bidsmreye.py

@@ -15,13 +15,15 @@
 from bidsmreye.prepare_data import prepare_data
 from bidsmreye.utils import bidsmreye_log
 from bidsmreye.utils import Config
+from bidsmreye.utils import default_log_level
+from bidsmreye.utils import log_levels
 
 __version__ = _version.get_versions()["version"]
 
 log = bidsmreye_log(name="bidsmreye")
 
 
-def main(argv: Any = sys.argv) -> None:
+def cli(argv: Any = sys.argv) -> None:
     """Run the bids app.
 
     :param argv: _description_, defaults to sys.argv
@@ -46,9 +48,15 @@ def main(argv: Any = sys.argv) -> None:
         bids_filter=args.bids_filter_file,
     )  # type: ignore
 
-    log_level = "DEBUG" if cfg.debug else args.verbosity
-
-    log.setLevel(log_level)
+    # TODO integrate as part of base config
+    # https://stackoverflow.com/a/53293042/14223310
+    log_level = log_levels().index(default_log_level())
+    # For each "-v" flag, adjust the logging verbosity accordingly
+    # making sure to clamp off the value from 0 to 4, inclusive of both
+    for adjustment in args.log_level or ():
+        log_level = min(len(log_levels()) - 1, max(log_level + adjustment, 0))
+    log_level_name = log_levels()[log_level]
+    log.setLevel(log_level_name)
 
     log.info("Running bidsmreye version %s", __version__)
 
@@ -91,7 +99,7 @@ def common_parser() -> MuhParser:
         description="BIDS app using deepMReye to decode eye motion for fMRI time series data.",
         epilog="""
         For a more readable version of this help section,
-        see the online https://bidsmreye.readthedocs.io/".
+        see the online https://bidsmreye.readthedocs.io/.
         """,
     )
 
@@ -119,14 +127,7 @@ def common_parser() -> MuhParser:
     parser.add_argument(
         "--action",
         help="""
-        What action to perform:
-
-        - all:        run all steps
-
-        - prepare:    prepare data for analysis coregister to template,
-                      normalize and extract data
-
-        - generalize: generalize from data to give predicted labels
+        What action to perform.
         """,
         choices=["all", "prepare", "generalize"],
         default="all",
@@ -174,21 +175,19 @@ def common_parser() -> MuhParser:
         nargs="+",
     )
     parser.add_argument(
-        "--verbosity",
-        help="ERROR, INFO, WARNING, DEBUG",
-        choices=["ERROR", "INFO", "WARNING", "DEBUG"],
-        default="INFO",
-    )
-    parser.add_argument(
-        "--debug", help="true or false.", choices=["true", "false"], default="false"
+        "-v",
+        "--verbose",
+        dest="log_level",
+        action="append_const",
+        const=-1,
     )
+    parser.add_argument("--debug", help="Switch to debug mode", action="store_true")
     parser.add_argument(
         "--reset_database",
         help="""
         Resets the database of the input dataset.
         """,
-        choices=["true", "false"],
-        default="false",
+        action="store_true",
     )
     parser.add_argument(
         "--bids_filter_file",
@@ -222,7 +221,3 @@ def common_parser() -> MuhParser:
     )
 
     return parser
-
-
-if __name__ == "__main__":
-    main()

bidsmreye/download.py

@@ -2,24 +2,37 @@
 from __future__ import annotations
 
 import argparse
+import sys
 from pathlib import Path
+from typing import Any
+from typing import IO
 
 import pkg_resources
 import pooch
+import rich
 
 from bidsmreye.utils import bidsmreye_log
 from bidsmreye.utils import move_file
 
 log = bidsmreye_log(name="bidsmreye")
 
 
-def main() -> None:
-    """Download the models from OSF.
+class MuhParser(argparse.ArgumentParser):
+    """Parser for the main script."""
 
-    :return: _description_
-    :rtype: _type_
-    """
-    parser = argparse.ArgumentParser(description="bidsMReye model downloader.")
+    def _print_message(self, message: str, file: IO[str] | None = None) -> None:
+        rich.print(message, file=file)
+
+
+def download_parser() -> MuhParser:
+    """Execute the main script."""
+    parser = MuhParser(
+        description="Download deepmreye pretrained model from OSF.",
+        epilog="""
+        For a more readable version of this help section,
+        see the online https://bidsmreye.readthedocs.io/.
+        """,
+    )
     parser.add_argument(
         "--model_name",
         help="""
@@ -44,7 +57,17 @@ def main() -> None:
         default=Path.cwd().joinpath("models"),
     )
 
-    args = parser.parse_args()
+    return parser
+
+
+def cli(argv: Any = sys.argv) -> None:
+    """Download the models from OSF.
+
+    :return: _description_
+    :rtype: _type_
+    """
+    parser = download_parser()
+    args = parser.parse_args(argv[1:])
 
     download(model_name=args.model_name, output_dir=args.output_dir)
 
@@ -77,7 +100,7 @@ def download(
         "4_pursuit": "96nyp",
         "5_free_viewing": "89nky",
         "6_1-to-5": "datasets_1to5.h5",
-        "7_1-to-6": "datasets_1to5.h5",
+        "7_1-to-6": "datasets_1to6.h5",
     }
 
     if model_name == "all":

bidsmreye/generalize.py

@@ -147,6 +147,8 @@ def process_subject(cfg: Config, layout_out: BIDSLayout, subject_label: str) ->
     if cfg.run:
         this_filter["run"] = return_regex(cfg.run)
 
+    log.info(f"Running subject: {subject_label}")
+
     log.debug(f"Looking for files with filter\n{this_filter}")
 
     data = layout_out.get(
@@ -155,7 +157,8 @@ def process_subject(cfg: Config, layout_out: BIDSLayout, subject_label: str) ->
         **this_filter,
     )
 
-    log.debug(f"Found files\n{data}")
+    to_print = [str(Path(x).relative_to(layout_out.root)) for x in data]
+    log.debug(f"Found files\n{to_print}")
 
     for file in data:
 

bidsmreye/prepare_data.py

@@ -145,11 +145,12 @@ def process_subject(
         **this_filter,
     )
 
-    log.debug(f"Found files\n{bf}")
+    to_print = [str(Path(x).relative_to(layout_in.root)) for x in bf]
+    log.debug(f"Found files\n{to_print}")
 
     for img in bf:
 
-        log.info(f"Processing {img}")
+        log.info(f"Processing file: {Path(img).name}")
 
         coregister_and_extract_data(img)
 

bidsmreye/templates/CITATION.mustache

@@ -6,4 +6,22 @@ to decode eye motion for fMRI time series data.
 
 ### data extraction
 
+All imaging data underwent co-registration conducted
+using Advanced Normalization Tools (ANTs, RRID:SCR_004757) within Python (ANTsPy).
+First, each participant's mean EPI was non-linearly co-registered
+to an average template.
+Second, we co-registered all voxels within a bounding box that included the eyes
+to a preselected bounding box in our group template to further improve the fit.
+
+Each voxel within those bounding box underwent two normalization steps.
+First, the across-run median signal intensity was subtracted
+from each voxel and sample
+and was divided by the median absolute deviation over time (temporal normalization).
+Second, for each sample, the mean across all voxels
+within the eye masks was subtracted and divided by the standard deviation
+across voxels (spatial normalization).
+
 ### eyemotion decoding
+
+Voxels time series were used as inputs for generalization decoding
+using using the the pre-trained model {{model}} from deepMReye ({{model_url}}).

bidsmreye/utils.py

@@ -24,6 +24,16 @@
 __version__ = _version.get_versions()["version"]
 
 
+def default_log_level() -> str:
+    """Return default log level."""
+    return "WARNING"
+
+
+def log_levels() -> list[str]:
+    """Return a list of log levels."""
+    return ["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]
+
+
 def bidsmreye_log(name: str | None = None) -> logging.Logger:
     """Create log.
 
@@ -38,7 +48,7 @@ def bidsmreye_log(name: str | None = None) -> logging.Logger:
 
     FORMAT = "bidsMReye - %(asctime)s - %(message)s"
 
-    log_level = "INFO"
+    log_level = default_log_level()
 
     if not name:
         name = "rich"
@@ -187,8 +197,11 @@ def move_file(input: Path, output: Path) -> None:
 
     :param output:
     :type output: Path
+
+    :param root: Optional. If specified, the printed path will be relative to this path.
+    :type root: Path
     """
-    log.info(f"{input.resolve()} --> {output.resolve()}")
+    log.debug(f"{input.resolve()} --> {output.resolve()}")
     create_dir_for_file(output)
     shutil.copy(input, output)
     input.unlink()
@@ -203,7 +216,7 @@ def create_dir_if_absent(output_path: str | Path) -> None:
     if isinstance(output_path, str):
         output_path = Path(output_path)
     if not output_path.is_dir():
-        log.info(f"Creating dir: {output_path}")
+        log.debug(f"Creating dir: {output_path}")
     output_path.mkdir(parents=True, exist_ok=True)